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Create PK Concentration Dataset

Source: R/format_data.R
format_pkncaconc_data.Rd

This function creates a pharmacokinetic concentration dataset from the provided ADNCA data.

Usage

format_pkncaconc_data(
  ADNCA,
  group_columns,
  time_column = "AFRLT",
  rrlt_column = "ARRLT",
  route_column = "ROUTE",
  time_end_column = NULL,
  nca_exclude_reason_columns = NULL
)

Arguments

ADNCA

A data frame containing the ADNCA data.

group_columns

A character vector specifying the columns to group by.

time_column

A character string specifying the time column.

rrlt_column

A character string specifying the time since last dose column.

route_column

A character string specifying the route column.

time_end_column

(Optional) A character string specifying the column for end time, used to calculate CONCDUR.

nca_exclude_reason_columns

A character vector specifying the columns to indicate reasons for excluding records from NCA analysis.

Value

A data frame containing the filtered and processed concentration data. The following new columns are created:

  • DOSNOA: Sequential dose number within each group, based on time of dose.

  • std_route: Standardized route, either "intravascular" or "extravascular", derived from the route column.

  • nca_exclude: Character column with concatenated exclusion reasons (if nca_exclude_reason_columns is provided), otherwise empty string.

  • CONCDUR: (Optional) Sampling duration, calculated as time_end_column - time_column if time_end_column is provided.

Details

The function performs the following steps:

  • Checks for required columns and data.

  • Filters out rows with EVID = 0 and PARAMCD containing "DOSE" (removes dosing data; not CDISC standard).

  • Optionally creates CONCDUR if time_end_column is provided.

  • Optionally creates nca_exclude by merging specified exclusion reason columns.

  • Creates DOSNOA variable: sequential numbers based on time of dose within each group.

  • Creates a std_route column with PKNCA values "intravascular" or "extravascular" based on the route column (ROUTE, CDISC: C66729).

  • Arranges the data by group_columns and dose time.

Examples

adnca <- read.csv(system.file("shiny/data/example-ADNCA.csv", package = "aNCA"))
conc_data <- format_pkncaconc_data(
  ADNCA = adnca,
  group_columns = c("STUDYID", "DOSETRT", "USUBJID", "PARAM"),
  time_column = "AFRLT",
  rrlt_column = "ARRLT",
  route_column = "ROUTE"
)